test_that("ard_continuous() works", { expect_error( ard_test <- ard_continuous(mtcars, variables = c(mpg, hp), by = c(am, vs)), NA ) expect_snapshot(class(ard_test)) expect_equal( get_ard_statistics( ard_test, group1_level %in% 0, group2_level %in% 0, variable %in% "mpg", stat_name %in% c("N", "mean") ), list( N = with(mtcars, length(mpg[am %in% 0 & vs %in% 0])), mean = with(mtcars, mean(mpg[am %in% 0 & vs %in% 0])) ), ignore_attr = TRUE ) expect_equal( ard_continuous( mtcars, variables = starts_with("xxxxx") ), dplyr::tibble() ) }) test_that("ard_continuous(fmt_fn) argument works", { ard_continuous( ADSL, variables = "AGE", statistic = list(AGE = continuous_summary_fns(c("N", "mean", "median"))), fmt_fn = list( AGE = list( mean = function(x) round5(x, digits = 3) |> as.character(), N = function(x) format(round5(x, digits = 2), nsmall = 2), N_obs = function(x) format(round5(x, digits = 2), nsmall = 2) ) ) ) |> apply_fmt_fn() |> dplyr::select(variable, stat_name, stat, stat_fmt) |> as.data.frame() |> expect_snapshot() ard_continuous( ADSL, variables = c("AGE", "BMIBL"), statistic = ~ continuous_summary_fns("mean"), fmt_fn = list( AGE = list( mean = function(x) round5(x, digits = 3) |> as.character() ) ) ) |> apply_fmt_fn() |> dplyr::select(variable, stat_name, stat, stat_fmt) |> as.data.frame() |> expect_snapshot() # tidyselect works ard_continuous( ADSL, variables = c("AGE", "BMIBL"), statistic = ~ continuous_summary_fns(c("mean", "sd")), fmt_fn = ~ list(~ function(x) round(x, 4)) ) |> apply_fmt_fn() |> dplyr::select(variable, stat_name, stat, stat_fmt) |> as.data.frame() |> expect_snapshot() }) test_that("ard_continuous() messaging", { # proper error message when statistic argument mis-specified expect_snapshot( ard_continuous(mtcars, variables = "mpg", statistic = ~ list(mean = "this is a string")), error = TRUE ) # proper error message when non-data frame passed expect_snapshot( ard_continuous(letters, variables = "mpg"), error = TRUE ) # proper error message when variables not passed expect_snapshot( ard_continuous(mtcars), error = TRUE ) }) test_that("ard_continuous(stat_label) argument works", { # formula expect_snapshot( ard_continuous( data = ADSL, by = "ARM", variables = c("AGE", "BMIBL"), stat_label = everything() ~ list(c("min", "max") ~ "min - max") ) |> as.data.frame() |> dplyr::select(stat_name, stat_label) |> dplyr::filter(stat_name %in% c("min", "max")) |> unique() ) # list expect_snapshot( ard_continuous( data = ADSL, by = "ARM", variables = c("AGE", "BMIBL"), stat_label = everything() ~ list(p25 = "25th %ile", p75 = "75th %ile") ) |> as.data.frame() |> dplyr::select(stat_name, stat_label) |> dplyr::filter(stat_name %in% c("p25", "p75")) |> unique() ) # variable-specific expect_snapshot( ard_continuous( data = ADSL, by = "ARM", variables = c("AGE", "BMIBL"), stat_label = AGE ~ list(p25 = "25th %ile", p75 = "75th %ile") ) |> as.data.frame() |> dplyr::filter(stat_name %in% c("p25", "p75")) |> dplyr::select(variable, stat_name, stat_label) |> unique() ) # statistics returns a named list of summaries conf_int <- function(x) { t.test(x)[["conf.int"]] |> as.list() |> rlang::set_names(c("conf.low", "conf.high")) } ard1 <- ard_continuous( ADSL, variables = "AGE", statistic = ~ list(conf.int = conf_int), stat_label = ~ list(conf.low = "LB", conf.high = "UB") ) |> dplyr::select(variable, stat_name, stat_label) |> as.data.frame() expect_snapshot(ard1) ard2 <- ard_continuous( ADSL, variables = "AGE", statistic = ~ list(conf.int = conf_int), stat_label = ~ list("conf.low" ~ "LB", "conf.high" ~ "UB") ) |> dplyr::select(variable, stat_name, stat_label) |> as.data.frame() expect_equal(ard1, ard2) }) test_that("ard_continuous() and ARD column names", { ard_colnames <- c( "group1", "group1_level", "variable", "variable_level", "context", "stat_name", "stat_label", "statistic", "fmt_fn", "warning", "error" ) # no errors when these variables are the summary vars expect_error( { df <- mtcars names(df) <- ard_colnames ard_continuous( data = suppressMessages(cbind(mtcars["am"], df)), variables = all_of(ard_colnames), by = "am" ) }, NA ) # no errors when these vars are the by var expect_error( { lapply( ard_colnames, function(byvar) { df <- mtcars[c("am", "mpg")] names(df) <- c(byvar, "mpg") ard_continuous( data = df, by = all_of(byvar), variables = "mpg" ) } ) }, NA ) }) test_that("ard_continuous() with grouped data works", { expect_equal( ADSL |> dplyr::group_by(ARM) |> ard_continuous(variables = AGE), ard_continuous(data = ADSL, by = ARM, variables = AGE) ) }) test_that("ard_continuous() with dates works and displays as expected", { ard_date <- ADSL |> ard_continuous( variables = DISONSDT, statistic = ~ continuous_summary_fns(c("min", "max", "sd")) ) expect_snapshot(ard_date) expect_equal(ard_date$stat[[1]], as.Date("1998-06-13")) }) test_that("ard_continuous() with empty/missing dates works, and preserves Date class", { empty_date <- data.frame(dt = as.Date(NA)) |> ard_continuous( variables = dt, statistic = ~ continuous_summary_fns(c("min")) ) expect_equal(inherits(empty_date$stat[[1]], "Date"), TRUE) }) test_that("ard_continuous() works with non-syntactic names", { expect_equal( ADSL |> dplyr::mutate(`BMI base` = BMIBL, `Age` = AGE) |> ard_continuous( variables = `BMI base`, statistic = ~ continuous_summary_fns(c("min", "max", "sd")) ) |> dplyr::select(stat, error), ADSL |> ard_continuous( variables = BMIBL, statistic = ~ continuous_summary_fns(c("min", "max", "sd")) ) |> dplyr::select(stat, error) ) expect_equal( ADSL |> dplyr::mutate(`BMI base` = BMIBL, `Age` = AGE) |> ard_continuous( variables = "BMI base", statistic = ~ continuous_summary_fns(c("min", "max", "sd")) ) |> dplyr::select(stat, error), ADSL |> ard_continuous( variables = BMIBL, statistic = ~ continuous_summary_fns(c("min", "max", "sd")) ) |> dplyr::select(stat, error) ) `mean error` <- function(x) { stop("There was an error calculating the mean.") mean(x) } expect_snapshot(ADSL |> dplyr::mutate(`BMI base` = BMIBL, `Age` = AGE, `Arm Var` = ARM) |> ard_continuous( variables = c("BMI base", `Age`), statistic = ~ list("mean lbl" = `mean error`), stat_label = everything() ~ list(`mean lbl` = "Test lbl") ) |> as.data.frame()) }) # - test if function parameters can be used as variable names without error test_that("ard_continuous() works when using generic names ", { mtcars2 <- mtcars %>% dplyr::rename("variable_level" = mpg, "variable" = cyl, "median" = disp, "p25" = gear) expect_equal( ard_continuous(mtcars, variables = c(mpg, cyl), by = disp) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(variable_level, variable), by = median) |> dplyr::select(stat) ) expect_equal( ard_continuous(mtcars, variables = c(disp, gear), by = mpg) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(median, p25), by = variable_level) |> dplyr::select(stat) ) expect_equal( ard_continuous(mtcars, variables = c(disp, gear), by = cyl) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(median, p25), by = variable) |> dplyr::select(stat) ) expect_equal( ard_continuous(mtcars, variables = c(disp, mpg), by = gear) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(median, variable_level), by = p25) |> dplyr::select(stat) ) # rename vars mtcars2 <- mtcars %>% dplyr::rename("by" = mpg, "statistic" = cyl, "weights" = disp, "p75" = gear) expect_equal( ard_continuous(mtcars, variables = c(mpg, cyl), by = disp) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(by, statistic), by = weights) |> dplyr::select(stat) ) expect_equal( ard_continuous(mtcars, variables = c(cyl, disp), by = mpg) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(statistic, weights), by = by) |> dplyr::select(stat) ) expect_equal( ard_continuous(mtcars, variables = c(mpg, gear), by = cyl) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(by, p75), by = statistic) |> dplyr::select(stat) ) expect_equal( ard_continuous(mtcars, variables = c(mpg, cyl), by = gear) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(by, statistic), by = p75) |> dplyr::select(stat) ) expect_equal( ard_continuous(mtcars, variables = c(mpg, gear), by = cyl) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(by, p75), by = statistic) |> dplyr::select(stat) ) # rename vars mtcars2 <- mtcars %>% dplyr::rename("mean" = mpg, "sd" = cyl, "var" = disp, "sum" = gear) expect_equal( ard_continuous(mtcars, variables = c(mpg, cyl), by = disp) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(mean, sd), by = var) |> dplyr::select(stat) ) expect_equal( ard_continuous(mtcars, variables = c(cyl, disp), by = mpg) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(sd, var), by = mean) |> dplyr::select(stat) ) expect_equal( ard_continuous(mtcars, variables = c(mpg, disp), by = cyl) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(mean, var), by = sd) |> dplyr::select(stat) ) expect_equal( ard_continuous(mtcars, variables = c(mpg, cyl), by = gear) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(mean, sd), by = sum) |> dplyr::select(stat) ) expect_equal( ard_continuous(mtcars, variables = c(mpg, gear), by = cyl) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(mean, sum), by = sd) |> dplyr::select(stat) ) # rename vars mtcars2 <- mtcars %>% dplyr::rename("deff" = mpg, "min" = cyl, "max" = disp, "mean.std.error" = gear) expect_equal( ard_continuous(mtcars, variables = c(mpg, cyl), by = disp) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(deff, min), by = max) |> dplyr::select(stat) ) expect_equal( ard_continuous(mtcars, variables = c(cyl, disp), by = mpg) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(min, max), by = deff) |> dplyr::select(stat) ) expect_equal( ard_continuous(mtcars, variables = c(mpg, disp), by = cyl) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(deff, max), by = min) |> dplyr::select(stat) ) expect_equal( ard_continuous(mtcars, variables = c(mpg, cyl), by = gear) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(deff, min), by = mean.std.error) |> dplyr::select(stat) ) expect_equal( ard_continuous(mtcars, variables = c(mpg, gear), by = cyl) |> dplyr::select(stat), ard_continuous(mtcars2, variables = c(deff, mean.std.error), by = min) |> dplyr::select(stat) ) })